It's one of those mysteries that has no real answer. The most likely answer is that it's from some kind of dragon considering the location or perhaps it belongs to a more powerful form of giant that was wiped out amidst the war with the dragons. Sadly it's never been referenced again and there's no strong theory on the skull.

I always found it too humanoid to consider it to be from a dragon, so my bet would be that it's from a giant. Granted, it would be from a particularly large and bestial variety of giant but considering how varied in size and morphology giants are in the Dark Souls games it's not exactly outside the realm of possibility.